How do I make an NMDS chart?

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How do I make an NMDS chart?

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I'd like to show the species in the NMDS chart. I can only show the points of the communities in each group, but I would like to show the species. My chart looks like this:

r ggplot2

asked by anonymous 02.08.2018 / 21:21

1 answer

Is it wrong to return null in a Task? How do I add the values stored in the list: pairs?

score 1 · Answer 1

Check the introduction sticker for the vegan package:

vignette("intro-vegan", "vegan")

Using the example provided by the package:

library(vegan)
data(dune)
nmds <- metaMDS(dune)
plot(nmds, type = "n"); text(nmds, display = "spec")

Ifyouwanttouseggplot2togeneratethegraphs,thesimplestoptionistousetheggveganpackage.Itisstillunderdevelopment,butcanbeinstalledfromGitHub:

library(devtools);install_github("gavinsimpson/ggvegan")

It implements autoplot methods for objects generated by vegan. In case:

library(ggvegan)
autoplot(nmds, geom = "text", layers = "species")

Inthecurrentstateofdevelopment,ifyouneedtoaddseveralotherelementstothechart(suchasellipses),itbecomeseasiertouseplot.

Athirdoptionisthefactoextrapackage.Itgeneratesgreatviewsformultivariateanalysisinasimpleway.ButithasnoNMDSmethods,justasitdoesnotsupportvegan-generatedobjects.Butworthknowing: link